PyOpenMS-Viz#
Welcome to PyOpenMS-Viz Documentation! PyOpenMS-Viz is a visualization package for mass spectrometry data directly from pandas dataframes
Key Features Include:
DataFrame Based Plotting - Plot directly from a pandas dataframe object
Interactive and Static Plotting - Multiple backends supported including matplotlib, bokeh and plotly.
Usage Flexibility - User-friendly web based dashboard for quick visualizations, advanced python package for more complex applications
Quick Start#
Installation#
pip install pyopenms-viz
Plotting a Spectrum#
import pandas as pd
ms_data = pd.read_csv("path/to/ms_data.csv")
pd.set_option("plotting.backend", "ms_bokeh") # try changing backend to "ms_plotly" or "ms_matplotlib"
ms_data.plot(x="m/z", y="intensity", kind="spectrum")
Plotting a Chromatogram#
import pandas as pd
ms_data = pd.read_csv("path/to/ms_data.csv")
pd.set_option("plotting.backend", "ms_bokeh") # try changing backend to "ms_plotly" or "ms_matplotlib"
ms_data.plot(x="rt", y="intensity", kind="chromatogram")
Support#
If you are having issues or would like to propose a new feature, please use the issues tracker.
License#
This project is licensed under the BSD 3-Clause license.
Citation#
If PyOpenMS-Viz was usefull in your research please cite the following: